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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ), 'gf_id' => 'HOM05D001569', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001569' ), 'data_identifier' => 'HOM05D001569', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001569', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '407', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p41280' => 'bna', 'A03p03260' => 'bna', 'A05p43460' => 'bna', 'A10p21340' => 'bna', 'A10p29180' => 'bna', 'Aa31LG11G11440' => 'aar', 'Aa31LG11G1780' => 'aar', 'Aa31LG3G18950' => 'aar', 'Aa31LG5G14490' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1187' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.1829' => 'aag', 'Actinidia01033' => 'ach', 'Actinidia13624' => 'ach', 'Actinidia17305' => 'ach', 'Actinidia31762' => 'ach', 'Actinidia38616' => 'ach', 'Ah.04g153190' => 'amhyb', 'Ah.13g075340' => 'amhyb', 'AL3G13800' => 'aly', 'AL6G17740' => 'aly', 'AL6G29370' => 'aly', 'Aqoxy180s011' => 'aox', 'Aqoxy1G00485' => 'aox', 'Aqoxy3G02654' => 'aox', 'arahy.Tifrunner.gnm1.ann1.03A2T4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8EFC3U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HSU2LT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J1NXPM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TH581T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WE6MWD' => 'arhy', 'AT3G03910' => 'ath', 'AT5G07440' => 'ath', 'AT5G18170' => 'ath', 'ATR0665G618' => 'atr', 'ATR0697G131' => 'atr', 'Atru.chr4.2980' => 'acertr', 'Atru.chr6.1974' => 'acertr', 'Atru.chr9.1209' => 'acertr', 'AUR62032053' => 'cqu', 'AUR62032691' => 'cqu', 'BcaB01g05702' => 'bca', 'BcaB01g06039' => 'bca', 'BcaB05g21617' => 'bca', 'BcaB08g36699' => 'bca', 'BcaB08g36700' => 'bca', 'BcaC04g18717' => 'bca', 'BcaC04g18719' => 'bca', 'BcaC05g28336' => 'bca', 'BcaC05g29892' => 'bca', 'BcaC05g29896' => 'bca', 'BcaC06g32438' => 'bca', 'BcaC06g32475' => 'bca', 'BcaNung02105' => 'bca', 'BcaNung05742' => 'bca', 'BcaNung05744' => 'bca', 'BNapus_Darmor_BZH_scaffold_78p00430' => 'bna', 'BolC1t05800H' => 'bol', 'BolC2t06275H' => 'bol', 'BolC3t12907H' => 'bol', 'BolC5t34966H' => 'bol', 'BolC5t34970H' => 'bol', 'BolC7t44555H' => 'bol', 'BolC9t58723H' => 'bol', 'BolC9t59700H' => 'bol', 'BraA01t04551Z' => 'bra', 'BraA02t04919Z' => 'bra', 'BraA03t09678Z' => 'bra', 'BraA05t23086Z' => 'bra', 'BraA10t44197Z' => 'bra', 'BraA10t44965Z' => 'bra', 'C01p45930' => 'bna', 'C02p03130' => 'bna', 'C03p03690' => 'bna', 'C09p58810' => 'bna', 'C09p69570' => 'bna', 'CAN.G248.52' => 'can', 'CAN.G297.13' => 'can', 'CAN.G503.23' => 'can', 'CAN.G960.48' => 'can', 'CANSAT21G2237' => 'cansat', 'CANSAT56G1247' => 'cansat', 'CANSAT78G2354' => 'cansat', 'CARHR078030' => 'chi', 'CARHR194890' => 'chi', 'CARHR205710' => 'chi', 'Carub.0003s0315' => 'cru', 'Carub.0006s0641' => 'cru', 'Carub.0006s1645' => 'cru', 'Ca_02570_v3' => 'car', 'Ca_04489_v3' => 'car', 'Ca_08266_v3' => 'car', 'Ca_22014_v3' => 'car', 'Ca_24612_v3' => 'car', 'Ca_30501_v3' => 'car', 'CBR_g19527' => 'cbr', 'CBR_g34345' => 'cbr', 'Cc00_g13050' => 'ccan', 'Cc00_g14810' => 'ccan', 'Cc06_g22970' => 'ccan', 'Cc07_g20860' => 'ccan', 'CDE06G2218' => 'cde', 'CDE07G1124' => 'cde', 'CDE08G0423' => 'cde', 'Cfa012325' => 'cfa', 'Cfa013606' => 'cfa', 'Cfa016442' => 'cfa', 'Ciclev10020390m.g' => 'ccl', 'Ciclev10020428m.g' => 'ccl', 'Ciclev10031681m.g' => 'ccl', 'CiPaw.07G182900' => 'cil', 'CiPaw.08G042800' => 'cil', 'CiPaw.09G002000' => 'cil', 'CiPaw.11G072800' => 'cil', 'ClCG01G004910' => 'cla', 'ClCG04G005320' => 'cla', 'ClCG07G017180' => 'cla', 'COL.COLO4_13596' => 'col', 'COL.COLO4_37306' => 'col', 'Cpa.g.sc13.219' => 'cpa', 'Cpa.g.sc51.115' => 'cpa', 'Cpa.g.sc98.28' => 'cpa', 'Cre05.g232150' => 'cre', 'Cre09.g388800' => 'cre', 'CsaV3_4G004380' => 'csa', 'CsaV3_4G013270' => 'csa', 'CsaV3_5G005130' => 'csa', 'CSS0000661' => 'camsi', 'CSS0002543' => 'camsi', 'CSS0007238' => 'camsi', 'CSS0022051' => 'camsi', 'CSS0034454' => 'camsi', 'CSS0046767' => 'camsi', 'CSS0049880' => 'camsi', 'DCAR_014646' => 'dca', 'DCAR_018071' => 'dca', 'DCAR_019878' => 'dca', 'DCAR_020164' => 'dca', 'Dinv14578' => 'din', 'Dinv16895' => 'din', 'Dinv34532' => 'din', 'Dinv37015' => 'din', 'Duzib068G1148' => 'dzi', 'Duzib084G0990' => 'dzi', 'Duzib106G1610' => 'dzi', 'Duzib177G0245' => 'dzi', 'Duzib177G0495' => 'dzi', 'Duzib177G0884' => 'dzi', 'Duzib205G1789' => 'dzi', 'ECA233G2177' => 'eca', 'ECA233G4663' => 'eca', 'ECA238G3036' => 'eca', 'EL10Ac3g06821' => 'bvu', 'Eucgr.A02097' => 'egr', 'Eucgr.A02935' => 'egr', 'FAN03G0798' => 'fan', 'FAN04G0629' => 'fan', 'FAN06G2931' => 'fan', 'FAN08G1921' => 'fan', 'FAN13G0301' => 'fan', 'FAN18G1718' => 'fan', 'FAN19G0659' => 'fan', 'FAN23G3001' => 'fan', 'FAN26G2840' => 'fan', 'FAN28G0759' => 'fan', 'FAN28G2254' => 'fan', 'FvH4_1g28120' => 'fve', 'FvH4_5g20340' => 'fve', 'FvH4_7g26540' => 'fve', 'Glyma.01G204600' => 'gma', 'Glyma.02G072200' => 'gma', 'Glyma.05G066200' => 'gma', 'Glyma.11G161529' => 'gma', 'Glyma.16G041200' => 'gma', 'Glyma.16G153400' => 'gma', 'Glyma.17G148000' => 'gma', 'Glyma.19G111000' => 'gma', 'Gohir.A03G061200' => 'ghi', 'Gohir.A08G213100' => 'ghi', 'Gohir.A11G259600' => 'ghi', 'Gohir.A12G195700' => 'ghi', 'Gohir.A12G212900' => 'ghi', 'Gohir.D03G104800' => 'ghi', 'Gohir.D08G230200' => 'ghi', 'Gohir.D11G269700' => 'ghi', 'Gohir.D12G198500' => 'ghi', 'Gohir.D12G215400' => 'ghi', 'Gorai.003G110800' => 'gra', 'Gorai.004G244400' => 'gra', 'Gorai.007G289700' => 'gra', 'Gorai.008G213200' => 'gra', 'Gorai.008G231000' => 'gra', 'GSVIVG01003691001' => 'vvi', 'GSVIVG01004635001' => 'vvi', 'GSVIVG01004636001' => 'vvi', 'GSVIVG01024475001' => 'vvi', 'GSVIVG01024479001' => 'vvi', 'GSVIVG01024480001' => 'vvi', 'GSVIVG01024481001' => 'vvi', 'GSVIVG01033402001' => 'vvi', 'HanXRQChr01g0015171' => 'han', 'HanXRQChr05g0129711' => 'han', 'HanXRQChr05g0144391' => 'han', 'HanXRQChr08g0223371' => 'han', 'HanXRQChr09g0266381' => 'han', 'Haze_08371' => 'cav', 'Haze_19419' => 'cav', 'Haze_19448' => 'cav', 'Haze_22227' => 'cav', 'Haze_26907' => 'cav', 'Hma1.2p1_1014F.1_g247890' => 'hma', 'Hma1.2p1_2647F.1_g326060' => 'hma', 'HPP92_012141' => 'vpl', 'HPP92_015637' => 'vpl', 'HPP92_020917' => 'vpl', 'Hund06014' => 'sun', 'Hund19235' => 'sun', 'Hund24834' => 'sun', 'Lalb_Chr02g0157111' => 'lal', 'Lalb_Chr05g0214221' => 'lal', 'Lalb_Chr09g0324161' => 'lal', 'Lalb_Chr09g0329791' => 'lal', 'Lalb_Chr14g0364481' => 'lal', 'Lalb_Chr16g0386431' => 'lal', 'Lalb_Chr22g0359181' => 'lal', 'Lj1A972T39' => 'lonja', 'Lj1A973T45' => 'lonja', 'Lj1g0010014' => 'lja', 'Lj2A358T45' => 'lonja', 'Lj2g0026992' => 'lja', 'Lj4g0018858' => 'lja', 'Lj8C49T14' => 'lonja', 'Lsat_1_v5_gn_2_57620' => 'lsa', 'Lsat_1_v5_gn_8_11521' => 'lsa', 'Manes.06G129700' => 'mes', 'Manes.08G144100' => 'mes', 'Manes.09G141500' => 'mes', 'Manes.14G041300' => 'mes', 'Mapoly0023s0133' => 'mpo', 'Mapoly0103s0068' => 'mpo', 'MBI04_g13854_MAGBIO' => 'mbi', 'MBI05_g05615_MAGBIO' => 'mbi', 'MD00G1113900' => 'mdo', 'MD00G1175600' => 'mdo', 'MD00G1175700' => 'mdo', 'MD01G1174400' => 'mdo', 'MD04G1055700' => 'mdo', 'MD04G1241400' => 'mdo', 'MD05G1237100' => 'mdo', 'MD06G1047200' => 'mdo', 'MD06G1140900' => 'mdo', 'MD07G1241100' => 'mdo', 'MD10G1043700' => 'mdo', 'MD10G1307200' => 'mdo', 'MD12G1003600' => 'mdo', 'MD13G1107100' => 'mdo', 'MD14G1002500' => 'mdo', 'MD15G1086100' => 'mdo', 'MD15G1086200' => 'mdo', 'Medtr0016s0030' => 'mtr', 'Medtr4g099320' => 'mtr', 'Medtr5g013470' => 'mtr', 'Medtr6g029460' => 'mtr', 'Medtr7g085630' => 'mtr', 'MELO3C005444.2' => 'cme', 'MELO3C008802.2' => 'cme', 'MELO3C017628.2' => 'cme', 'Migut.F00544' => 'egut', 'Migut.F01211' => 'egut', 'Migut.J01887' => 'egut', 'MSTRG.149' => 'ama', 'Nitab4.5_0000103g0200' => 'nta', 'Nitab4.5_0000375g0370' => 'nta', 'Nitab4.5_0002236g0060' => 'nta', 'Nitab4.5_0002359g0020' => 'nta', 'Nitab4.5_0002769g0080' => 'nta', 'Nitab4.5_0004099g0020' => 'nta', 'Nitab4.5_0004844g0040' => 'nta', 'Nitab4.5_0007542g0020' => 'nta', 'Nitab4.5_0009048g0020' => 'nta', 'Nitab4.5_0014508g0010' => 'nta', 'Nn1g00764' => 'nnu', 'Nn2g15867' => 'nnu', 'Nn6g33761' => 'nnu', 'Nn7g35852' => 'nnu', 'Oeu030872.1' => 'oeu', 'Oeu059995.1' => 'oeu', 'Os01g0358900' => 'osa', 'Os02g0650900' => 'osa', 'Os03g0794500' => 'osa', 'Os04g0543900' => 'osa', 'Peaxi162Scf00003g00482' => 'pax', 'Peaxi162Scf00073g00181' => 'pax', 'Peaxi162Scf00076g01042' => 'pax', 'Peaxi162Scf00167g01019' => 'pax', 'Peaxi162Scf00304g00091' => 'pax', 'PGR042G2945' => 'pgr', 'PGR042G3973' => 'pgr', 'PGSC0003DMG400008344' => 'stu', 'PGSC0003DMG400008356' => 'stu', 'PGSC0003DMG400016001' => 'stu', 'PGSC0003DMG400027589' => 'stu', 'Phvul.001G110500' => 'pvu', 'Phvul.003G225100' => 'pvu', 'Phvul.004G080200' => 'pvu', 'Potri.012G113500' => 'ptr', 'Potri.013G058300' => 'ptr', 'Potri.015G111000' => 'ptr', 'Potri.019G034800' => 'ptr', 'Pp3c13_16600' => 'ppa', 'Pp3c19_11670' => 'ppa', 'Pp3c3_20260' => 'ppa', 'Pp3c4_7960' => 'ppa', 'Pp3c4_7965' => 'ppa', 'Pp3c8_13280' => 'ppa', 'Prupe.2G269800' => 'ppe', 'Prupe.5G056900' => 'ppe', 'Prupe.7G004100' => 'ppe', 'Psat0s1971g0240' => 'psa', 'Psat1g096200' => 'psa', 'Psat2g175760' => 'psa', 'Psat2g175800' => 'psa', 'Psat4g075720' => 'psa', 'PSO063G3246' => 'pso', 'PSO339G1733' => 'pso', 'PSO384G0438' => 'pso', 'PSO675G0034' => 'pso', 'PSO732G0440' => 'pso', 'PSO782G4299' => 'pso', 'QL07p019523' => 'qlo', 'QL09p027349' => 'qlo', 'QL12p008800' => 'qlo', 'RcHm_v2.0_Chr1g0373211' => 'rch', 'RcHm_v2.0_Chr3g0497101' => 'rch', 'RcHm_v2.0_Chr7g0205521' => 'rch', 'Rhsim04G0087600' => 'rsi', 'Rhsim09G0188300' => 'rsi', 'Sabra12G0082700' => 'sbr', 'Sabra13G0051800' => 'sbr', 'Sabra15G0132800' => 'sbr', 'Sabra19G0042600' => 'sbr', 'Sabra19G0044900' => 'sbr', 'SalBow2G0929' => 'sbo', 'SalBow3G1905' => 'sbo', 'SalBow6G3301' => 'sbo', 'Sc09g0008000' => 'sci', 'Sc19g0006450' => 'sci', 'Sed0011156' => 'sed', 'Sed0016010' => 'sed', 'Sed0027274' => 'sed', 'SEGI_41245' => 'sgi', 'SGA_v2.0_scaffold236G43729' => 'sas', 'SGA_v2.0_scaffold44G16593' => 'sas', 'SGA_v2.0_scaffold60G20849' => 'sas', 'SGA_v2.0_scaffold69G23021' => 'sas', 'SMO164G0163' => 'smo', 'SMO226G0003' => 'smo', 'SMO292G0022' => 'smo', 'SMO302G0001' => 'smo', 'SMO302G0015' => 'smo', 'SMO302G0050' => 'smo', 'SMO361G0311' => 'smo', 'SMO361G0637' => 'smo', 'SMO364G0109' => 'smo', 'SMO367G0832' => 'smo', 'Solyc03g094010.3' => 'sly', 'Solyc05g052100.3' => 'sly', 'Solyc06g033860.2' => 'sly', 'Solyc10g078550.4' => 'sly', 'Sopen03g024860' => 'spe', 'Sopen05g030640' => 'spe', 'Sopen06g014160' => 'spe', 'Sopen10g029200' => 'spe', 'Sp3g02880' => 'spa', 'Sp6g26150' => 'spa', 'Sp6g35430' => 'spa', 'TAR272G0004' => 'tar', 'TAR375G1107' => 'tar', 'TAR623G0348' => 'tar', 'TAR633G2713' => 'tar', 'THA.LOC104801660' => 'tha', 'THA.LOC104802868' => 'tha', 'THA.LOC104821147' => 'tha', 'Thecc.03G145200' => 'tca', 'Thecc.03G240700' => 'tca', 'Thecc.05G294600' => 'tca', 'Thhalv10013679m.g' => 'esa', 'Thhalv10013680m.g' => 'esa', 'Thhalv10020857m.g' => 'esa', 'TPR.G169' => 'tpr', 'TPR.G17120' => 'tpr', 'TPR.G31427' => 'tpr', 'TPR.G34622' => 'tpr', 'TPR.G34624' => 'tpr', 'TPR.G5905' => 'tpr', 'TWI14G1182' => 'twi', 'TWI23G0258' => 'twi', 'TWI32G1129' => 'twi', 'unitig_0.g513' => 'ugi', 'unitig_37.g12483' => 'ugi', 'unitig_46.g18757' => 'ugi', 'vmacro09140' => 'vma', 'vmacro09931' => 'vma', 'VMungo0251G0504' => 'vmu', 'VMungo0464G0608' => 'vmu', 'VMungo1383G2821' => 'vmu', 'Zm00001eb060520' => 'zma', 'Zm00001eb427810' => 'zma' ) $gf_id = 'HOM05D001569' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001569' ) $data_identifier = 'HOM05D001569' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 5, 'amhyb' => (int) 2, 'aly' => (int) 3, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 4, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 1, 'egr' => (int) 2, 'fan' => (int) 11, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 8, 'han' => (int) 5, 'cav' => (int) 5, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 2, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mdo' => (int) 17, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 1, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 2, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 1, 'sas' => (int) 4, 'smo' => (int) 10, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 3, 'vma' => (int) 2, 'vmu' => (int) 3, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb427810' $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